[AMBER] Crashed dynamics : connectivity

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Wed, 15 May 2019 13:59:49 +0100

Dear all,

I am dealing with ion pairing phenomena, and for this reason I am
simulating a charged inorganic complex bound to cations (Li+, Na+, and
etc). I get the optimized structure from QM calculations and I use obabel
in order to convert it to mol2

obabel -ixyz input.xyz -omol2 output.mol2

 and then I only use output.mol2 for generating topology and coordinates,
so far so good. However, when I open prmtop and inpcrd (in VMD), I can see
that the cations, for example Li+, are not completely bound to the
molecule( peraphs it is just how MD assigns the bond lengths).
So, when I run the dynamics, this crashes, the bonds of Li+ with molecules
are ridiculously wrong.

May it be because the bespoke made frcmod.file does not contain any info
about Li-M ( M molecules) terms?
Also, I think that the output.mol2 probably doesn't have the correct info
about the connectivity of the systems ( bonds).

I wonder if anybody could give me any ny kind of hint on this. Much

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Received on Wed May 15 2019 - 06:30:04 PDT
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